diff --git a/Main/bin/runGeneCNVAndPloidyQuery b/Main/bin/runGeneCNVAndPloidyQuery
index 818dc8f29..d3d85e0a2 100755
--- a/Main/bin/runGeneCNVAndPloidyQuery
+++ b/Main/bin/runGeneCNVAndPloidyQuery
@@ -7,43 +7,30 @@ use GUS::ObjRelP::DbiDatabase;
 use GUS::Supported::GusConfig;
 use CBIL::Util::PropertySet;
 
-my ($gusConfigFile,$organismAbbrev,$geneSourceIdOrthologFile,$chrsForCalcsFile);
-&GetOptions("organismAbbrev=s" => \$organismAbbrev,
+my ($gusConfigFile,$taxonId,$orthoGroupFile,$geneSourceIdOrthologFile,$chrsForCalcsFile);
+&GetOptions("taxonId=s" => \$taxonId,
+            "orthoGroupFile=s" => \$orthoGroupFile,
             "geneSourceIdOrthologFile=s" => \$geneSourceIdOrthologFile,
             "chrsForCalcsFile=s" => \$chrsForCalcsFile);
-my $ploidy = 2;
-
-my $geneSourceSql = "with sequence as (
-                select gf.source_id as gene_source_id
-                , gf.na_feature_id
-                , ns.source_id as contig_source_id
-                , ns.source_id as sequence_source_id
-                , ns.TAXON_ID
-                from dots.genefeature gf
-                , DOTS.NASEQUENCE ns
-                , SRES.ONTOLOGYTERM ot
-                where gf.na_sequence_id = ns.na_sequence_id
-                and ot.name = 'chromosome'
-                and ns.SEQUENCE_ONTOLOGY_ID = ot.ONTOLOGY_TERM_ID
-                and ns.taxon_id = (select taxon_id from apidb.organism where abbrev = '$organismAbbrev')
-            ), orthologs as (
-                select gf.na_feature_id, sg.name
-                from dots.genefeature gf
-                , dots.SequenceSequenceGroup ssg
-                , dots.SequenceGroup sg
-                , core.TableInfo ti
-                where gf.na_feature_id = ssg.sequence_id
-                and ssg.sequence_group_id = sg.sequence_group_id
-                and ssg.source_table_id = ti.table_id
-                and ti.name = 'GeneFeature'
-            )
-            select s.gene_source_id
-            , o.name
-            from sequence s
-            , orthologs o
-            where s.na_feature_id = o.na_feature_id";
-
-my $chrsForCalcsSql = "select ns.source_id from dots.nasequence ns, sres.ontologyterm ot where ot.name = 'chromosome' and ot.ontology_term_id = ns.sequence_ontology_id and ns.taxon_id = (select taxon_id from apidb.organism where abbrev = '$organismAbbrev')";
+
+my $proteinToGeneSql = "
+SELECT aas.source_id AS protein_source_id,
+       gf.source_id  AS gene_source_id
+FROM dots.AASequence aas
+JOIN dots.TranslatedAASequence tas ON aas.aa_sequence_id = tas.aa_sequence_id
+JOIN dots.TranslatedAAFeature taf ON taf.aa_sequence_id = tas.aa_sequence_id
+JOIN dots.Transcript t ON taf.na_feature_id = t.na_feature_id
+JOIN dots.GeneFeature gf ON t.parent_id = gf.na_feature_id
+WHERE aas.subclass_view = 'TranslatedAASequence'
+  AND aas.taxon_id = $taxonId
+  AND aas.taxon_id IN (
+      SELECT taxon_id
+      FROM apidb.organism
+      WHERE is_annotated_genome = 1
+  )
+";
+
+my $chrsForCalcsSql = "select ns.source_id from dots.nasequence ns, sres.ontologyterm ot where ot.name = 'chromosome' and ot.ontology_term_id = ns.sequence_ontology_id and ns.taxon_id = $taxonId";
 
 $gusConfigFile = $ENV{GUS_HOME}."/config/gus.config";
 die "Config file $gusConfigFile does not exist" unless -e $gusConfigFile;
@@ -59,19 +46,50 @@ my $db = GUS::ObjRelP::DbiDatabase-> new($gusConfig->{props}->{dbiDsn},
 
 my $dbh = $db->getQueryHandle();
 
-my $orthoMclStmt = $dbh->prepare($geneSourceSql);
-$orthoMclStmt->execute();
+my $proteinToGeneStmt = $dbh->prepare($proteinToGeneSql);
+$proteinToGeneStmt->execute();
+
+my %proteinToGene;
+while (my @row = $proteinToGeneStmt->fetchrow_array()){
+    $proteinToGene{$row[0]} = $row[1];
+}
 
-open(GENE,">$geneSourceIdOrthologFile");
-while (my @row = $orthoMclStmt->fetchrow_array()){
-    print GENE "$row[0]\t$row[1]\n";
+my %proteinToGroup;
+open(GROUPS, "<$orthoGroupFile") or die "Cannot open $orthoGroupFile: $!";
+while (my $line = <GROUPS>) {
+    chomp $line;
+    my ($groupId, $proteinList) = split(/:\s*/, $line, 2);
+    next unless defined $proteinList;
+    foreach my $protein (split(/\s+/, $proteinList)) {
+        $proteinToGroup{$protein} = $groupId;
+    }
+}
+close GROUPS;
+
+my @proteinsWithNoGroup;
+open(GENE, ">$geneSourceIdOrthologFile") or die "Cannot open $geneSourceIdOrthologFile: $!";
+while (my ($protein, $gene) = each %proteinToGene) {
+    my $group = $proteinToGroup{$protein};
+    unless ($group) {
+        (my $altProtein = $protein) =~ s/:/\_/g;
+        $group = $proteinToGroup{$altProtein};
+    }
+    if ($group) {
+        print GENE "$gene\t$group\n";
+    } else {
+        push @proteinsWithNoGroup, $protein;
+    }
 }
 close GENE;
 
+if (@proteinsWithNoGroup) {
+    print STDERR "The following proteins have no group assignment in $orthoGroupFile:\n" . join("\n", @proteinsWithNoGroup) . "\n";
+}
+
 my $chrsForCalcs = $dbh->prepare($chrsForCalcsSql);
 $chrsForCalcs->execute();
 
-open(CHRS,">$chrsForCalcsFile");
+open(CHRS, ">$chrsForCalcsFile") or die "Cannot open $chrsForCalcsFile: $!";
 while (my @row = $chrsForCalcs->fetchrow_array()){
     print CHRS "$row[0]\t\n";
 }
diff --git a/Main/lib/perl/WorkflowSteps/UpdateOrthoPeripheralPersistentCache.pm b/Main/lib/perl/WorkflowSteps/UpdateOrthoPeripheralPersistentCache.pm
index 2c7cd538a..20d7c26f7 100644
--- a/Main/lib/perl/WorkflowSteps/UpdateOrthoPeripheralPersistentCache.pm
+++ b/Main/lib/perl/WorkflowSteps/UpdateOrthoPeripheralPersistentCache.pm
@@ -34,6 +34,7 @@ sub run {
 
       $self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/genesAndProteins/${nextflowWorkflow}_${nextflowBranch}/**/groupFastas  ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/");
 
+
       $self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/genesAndProteins/${nextflowWorkflow}_${nextflowBranch}/**/residualGroupFastas  ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/");
 
       $self->runCmd(0, "cp -r ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/genesAndProteins/${nextflowWorkflow}_${nextflowBranch}/**/newPeripheralDiamondCache/  ${preprocessedDataCache}/OrthoMCL/OrthoMCL_peripheralGroups/officialDiamondCache/peripheralCacheDir");